Metadata-Version: 1.1
Name: pathme
Version: 0.0.4
Summary: Harmonizing pathway databases using Biological Expression Language (BEL)
Home-page: https://github.com/ComPath/PathMe
Author: Daniel Domingo-Fernández, Sarah Mubeen, and Josep Marín-Llaó
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Description: PathMe |build| |coverage| |docs| |zenodo|
        =========================================
        The primary goal of this package is to convert KEGG, Reactome, and WikiPathways (see References below) to Biological
        Expression Language (BEL). PathMe is the continuation of the ComPath web application aimed at exploring, analyzing,
        and curating pathway knowledge in a gene-centric view. This different approach involves converting
        all the pathways to BEL as a pivotal integration schema to evaluate pathway cross-talks and consensus across
        multiple databases. Additionally, ComPath Reloaded is complemented with PathMe, a web application that enables the
        exploration of all the pathways from these resources using the mappings curated from ComPath.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        1. ``pathme`` can be installed with the following commands:
        
        .. code-block:: sh
        
            python3 -m pip install git+https://github.com/ComPath/PathMe.git@master
        
        2. or in editable mode with:
        
        .. code-block:: sh
        
            git clone https://github.com/ComPath/PathMe.git
        
        .. code-block:: sh
        
            cd pathme
        
        .. code-block:: sh
        
            python3 -m pip install -e .
        
        How to use
        ----------
        
        Each database has three main commands: "download", "bel", and "summarize":
        
        1. **Download content**
        
        PathMe first requires to download the raw files from the original pathway databases. This can be accomplished by
        running the command ('database' can be either KEGG, Reactome, or WikiPathways):
        
        .. code-block:: python
        
            python3 -m pathme 'database' download
        
        2. **Generate BEL Graphs**
        
        Once the raw files are downloaded, you can run the following to command to generate BELGraphs that will be exported
        as Python pickles files for further analysis. Furthermore, the conversion to BEL can be tuned differently for each
        database by using specific commands. For example, KEGG parameters are shown when running
        `python3 -m pathme kegg bel --help`.
        
        .. code-block:: python
        
            python3 -m pathme 'database' bel
        
        2. **Summarize**
        
        Summarizes the result of the conversion to BEL.
        
        .. code-block:: python
        
            python3 -m pathme 'database' summarize
        
        Advance parameters
        ------------------
        
        KEGG Functionalities
        ~~~~~~~~~~~~~~~~~~~~
        
        The KEGG module of PathMe is able to handle KGML differently depending on the goal. By default, KEGG groups
        together the complex of nodes (e.g., gene families) into one node as it is depicted in the KEGG cartoons and
        represented in the KGML files. However, this behavior can be modified by adding the parameter `--flatten=True`
        in the exporting command. Example:
        
        .. code-block:: python
        
            python3 -m pathme kegg bel --flatten=True
        
        
        References
        ----------
        
        KEGG
        ~~~~
        PathMe makes use of KEGG KGML files that are downloaded via the KEGG API for academic purposes (see `KEGG Terms and
        conditions <https://www.kegg.jp/kegg/rest/>`_.).
        
        - Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes,
          pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).
        - Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource
          for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
        - Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).
        
        Reactome
        ~~~~~~~~
        - Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016):
          D481–D487. PMC. Web. 6 Oct. 2017.
        - Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014):
          D472–D477. PMC. Web. 6 Oct. 2017.
        
        WikiPathways
        ~~~~~~~~~~~~
        - Slenter, D.N., et al WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research
          Nucleic Acids Research, (2017) doi.org/10.1093/nar/gkx1064
        - Kutmon, M., et al. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494
          (2016) doi:10.1093/nar/gkv1024
        - Kelder, T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012
          Jan;40(Database issue):D1301-7
        
        
        .. |build| image:: https://travis-ci.org/ComPath/PathMe.svg?branch=master
            :target: https://travis-ci.org/ComPath/PathMe
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/ComPath/PathMe/coverage.svg?branch=master
            :target: https://codecov.io/gh/ComPath/PathMe?branch=master
            :alt: Coverage Status
        
        .. |docs| image:: http://readthedocs.org/projects/pathme/badge/?version=latest
            :target: https://pathme.readthedocs.io/en/latest/
            :alt: Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/compath/pathme/badges/gpa.svg
            :target: https://codeclimate.com/github/compath/pathme
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/pathme.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/pathme.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/pathme.svg
            :alt: Apache-2.0
        
        .. |zenodo| image:: https://zenodo.org/badge/146161418.svg
            :target: https://zenodo.org/badge/latestdoi/146161418
        
Keywords: Pathways,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
